Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `HR41_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 175 MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU ILE 1 > ReadCoordsPdb(): Counting models in file `HR41_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file HR41_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 57560 ATOM records read from file > ReadCoordsPdb(): --> 57560 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET A 1 0.198 0.862 0.495 0.351 ALA A 2 0.782 0.107 ASP A 3 0.332 0.619 0.427 0.877 GLU A 4 0.999 0.996 0.762 0.869 0.976 4 4 ALA A 5 1.000 0.999 5 5 THR A 6 0.999 1.000 0.999 6 6 ARG A 7 0.999 0.998 0.999 0.752 0.723 0.737 1.000 7 7 ARG A 8 1.000 0.999 0.935 0.999 0.998 0.837 1.000 8 8 VAL A 9 0.999 0.999 1.000 9 9 VAL A 10 0.999 0.998 1.000 10 10 SER A 11 0.998 0.996 0.766 11 11 GLU A 12 0.997 0.983 0.999 0.918 0.958 12 12 ILE A 13 1.000 1.000 1.000 0.999 13 13 PRO A 14 0.999 0.997 1.000 1.000 14 14 VAL A 15 0.991 0.996 1.000 15 15 LEU A 16 0.995 0.987 0.997 0.988 16 16 LYS A 17 0.984 0.974 0.929 0.929 1.000 0.999 17 17 THR A 18 0.956 0.767 0.933 ASN A 19 0.757 0.916 0.493 0.619 ALA A 20 0.908 0.577 GLY A 21 0.649 0.987 PRO A 22 0.993 0.996 0.914 0.837 22 22 ARG A 23 0.998 0.998 0.999 0.870 0.574 0.652 1.000 23 23 ASP A 24 0.996 0.995 0.998 0.978 24 24 ARG A 25 1.000 0.999 1.000 0.998 0.523 0.564 1.000 25 25 GLU A 26 1.000 1.000 0.816 1.000 1.000 26 26 LEU A 27 1.000 0.999 0.899 0.921 27 27 TRP A 28 1.000 0.998 0.999 0.995 28 28 VAL A 29 1.000 1.000 1.000 29 29 GLN A 30 1.000 1.000 0.882 0.917 0.706 30 30 ARG A 31 0.999 0.998 0.756 0.745 0.490 0.051 0.998 31 31 LEU A 32 1.000 0.999 0.999 1.000 32 32 LYS A 33 1.000 0.999 1.000 1.000 1.000 1.000 33 33 GLU A 34 1.000 0.997 0.998 0.684 0.869 34 34 GLU A 35 1.000 0.997 0.491 0.339 0.691 35 35 TYR A 36 1.000 0.999 0.997 0.434 36 36 GLN A 37 1.000 1.000 1.000 0.851 0.976 37 37 SER A 38 1.000 1.000 0.918 38 38 LEU A 39 1.000 1.000 1.000 1.000 39 39 ILE A 40 0.999 1.000 1.000 1.000 40 40 ARG A 41 0.999 0.998 0.700 0.612 0.773 0.979 1.000 41 41 TYR A 42 0.999 0.998 0.997 0.930 42 42 VAL A 43 1.000 1.000 1.000 43 43 GLU A 44 1.000 0.998 0.652 0.923 0.942 44 44 ASN A 45 0.999 1.000 0.999 0.951 45 45 ASN A 46 0.998 0.998 0.952 0.650 46 46 LYS A 47 1.000 1.000 1.000 0.999 0.866 1.000 47 47 ASN A 48 0.999 1.000 0.999 0.921 48 48 ALA A 49 0.999 0.995 49 49 ASP A 50 1.000 1.000 0.906 0.958 50 50 ASN A 51 0.989 0.927 0.999 0.979 51 51 ASP A 52 0.943 0.976 0.873 0.988 52 52 TRP A 53 0.920 0.862 0.435 0.400 53 PHE A 54 0.997 0.988 0.818 0.891 54 54 ARG A 55 0.986 0.998 0.709 0.929 0.927 0.830 1.000 55 55 LEU A 56 0.996 0.996 0.686 0.725 56 56 GLU A 57 0.997 0.998 0.999 0.823 0.997 57 57 SER A 58 0.990 0.999 0.998 58 58 ASN A 59 0.998 0.997 0.656 0.982 59 59 LYS A 60 0.998 0.997 0.872 1.000 1.000 1.000 60 60 GLU A 61 0.998 0.997 0.999 0.999 0.965 61 61 GLY A 62 0.997 0.996 62 62 THR A 63 0.995 0.997 1.000 63 63 ARG A 64 0.993 0.999 0.998 0.998 0.932 0.995 1.000 64 64 TRP A 65 0.999 0.999 0.999 0.995 65 65 PHE A 66 0.999 0.981 0.995 0.797 66 66 GLY A 67 0.975 0.993 67 67 LYS A 68 0.998 0.993 0.411 0.990 0.425 0.936 68 68 CYS A 69 0.997 0.994 0.092 69 69 TRP A 70 0.971 0.994 0.440 0.114 70 70 TYR A 71 0.994 0.996 0.920 0.991 71 71 ILE A 72 0.993 1.000 0.999 0.464 72 72 HIS A 73 0.988 0.997 0.998 0.716 73 73 ASP A 74 0.996 0.641 0.905 0.987 LEU A 75 0.602 0.994 0.998 0.999 LEU A 76 0.996 0.960 0.996 0.999 76 76 LYS A 77 0.986 0.990 0.999 0.999 0.999 0.999 77 77 TYR A 78 0.956 0.987 0.653 0.595 78 78 GLU A 79 0.985 0.994 0.186 0.995 0.723 79 79 PHE A 80 0.997 0.995 0.999 0.501 80 80 ASP A 81 0.998 0.997 0.655 0.984 81 81 ILE A 82 0.999 0.997 0.998 0.881 82 82 GLU A 83 0.990 0.998 0.711 0.999 0.890 83 83 PHE A 84 0.985 0.998 0.860 0.899 84 84 ASP A 85 0.997 0.978 0.545 0.932 85 85 ILE A 86 0.999 0.999 0.999 1.000 86 86 PRO A 87 0.992 0.992 0.904 0.820 87 87 ILE A 88 0.999 0.995 0.840 1.000 88 88 THR A 89 0.994 0.990 0.998 89 89 TYR A 90 0.990 0.999 0.998 0.995 90 90 PRO A 91 0.998 0.989 1.000 0.999 91 91 THR A 92 0.993 0.999 1.000 92 92 THR A 93 0.993 0.993 1.000 93 93 ALA A 94 0.993 1.000 94 94 PRO A 95 0.989 0.984 0.938 0.895 95 95 GLU A 96 0.994 0.880 0.998 0.809 0.844 96 ILE A 97 0.878 0.994 0.999 0.957 97 ALA A 98 0.985 0.596 VAL A 99 0.604 0.994 0.915 PRO A 100 0.994 0.996 0.951 0.909 100 100 GLU A 101 0.993 0.992 0.601 0.319 0.839 101 101 LEU A 102 0.980 0.937 0.999 0.999 102 102 ASP A 103 0.927 0.668 0.792 0.907 GLY A 104 0.612 0.977 LYS A 105 0.991 0.965 0.994 0.511 0.997 0.762 105 105 THR A 106 0.913 0.563 0.407 ALA A 107 0.696 0.184 LYS A 108 0.687 0.629 0.796 0.670 0.934 0.792 MET A 109 0.743 0.798 0.627 0.324 0.288 TYR A 110 0.774 0.334 0.543 0.576 ARG A 111 0.517 0.619 0.582 0.758 0.668 0.778 1.000 GLY A 112 0.634 0.371 GLY A 113 0.258 0.787 LYS A 114 0.823 0.940 0.624 0.786 0.805 0.811 114 ILE A 115 0.940 0.988 0.841 1.000 115 115 CYS A 116 0.972 0.960 0.735 116 116 LEU A 117 0.984 0.826 0.998 0.915 117 THR A 118 0.888 0.973 0.274 118 ASP A 119 0.987 0.978 0.749 0.987 119 119 HIS A 120 0.980 0.969 0.923 0.913 120 120 PHE A 121 1.000 0.999 0.997 0.998 121 121 LYS A 122 1.000 1.000 0.752 1.000 1.000 1.000 122 122 PRO A 123 1.000 0.999 1.000 1.000 123 123 LEU A 124 1.000 0.999 0.999 1.000 124 124 TRP A 125 0.999 1.000 0.997 0.997 125 125 ALA A 126 1.000 0.999 126 126 ARG A 127 0.999 0.999 0.648 0.568 1.000 0.936 1.000 127 127 ASN A 128 0.984 0.880 0.997 0.991 128 VAL A 129 0.882 0.999 0.998 129 PRO A 130 0.996 0.961 0.999 0.999 130 130 LYS A 131 0.994 0.901 0.999 0.999 1.000 1.000 131 131 PHE A 132 0.922 0.960 0.837 0.798 132 132 GLY A 133 0.967 0.977 133 133 LEU A 134 0.996 0.998 0.929 0.926 134 134 ALA A 135 0.999 1.000 135 135 HIS A 136 1.000 0.999 0.998 0.967 136 136 LEU A 137 1.000 0.997 0.997 0.999 137 137 MET A 138 1.000 1.000 0.869 0.714 0.240 138 138 ALA A 139 0.998 0.999 139 139 LEU A 140 0.993 0.992 0.998 0.998 140 140 GLY A 141 0.996 0.997 141 141 LEU A 142 0.999 0.999 0.999 1.000 142 142 GLY A 143 0.999 0.999 143 143 PRO A 144 0.995 0.997 0.916 0.829 144 144 TRP A 145 1.000 1.000 0.999 0.999 145 145 LEU A 146 0.999 1.000 1.000 1.000 146 146 ALA A 147 1.000 0.996 147 147 VAL A 148 0.993 0.999 1.000 148 148 GLU A 149 0.952 0.971 0.664 0.612 0.744 149 149 ILE A 150 1.000 0.999 0.999 0.486 150 150 PRO A 151 0.989 0.992 0.913 0.840 151 151 ASP A 152 1.000 0.999 1.000 1.000 152 152 LEU A 153 1.000 0.999 0.730 0.408 153 153 ILE A 154 1.000 1.000 1.000 0.999 154 154 GLN A 155 1.000 1.000 0.789 0.661 0.880 155 155 LYS A 156 0.996 0.995 0.811 0.999 0.999 0.932 156 156 GLY A 157 0.990 0.992 157 157 VAL A 158 0.977 0.975 0.536 158 158 ILE A 159 0.963 0.988 0.998 0.625 159 159 GLN A 160 0.818 0.829 0.578 0.571 0.844 160 HIS A 161 0.843 0.552 0.414 0.523 LYS A 162 0.772 0.350 0.421 0.736 0.998 0.995 GLU A 163 0.265 0.692 0.403 0.589 0.914 LYS A 164 0.955 0.980 0.569 0.861 0.934 0.998 164 164 CYS A 165 0.417 0.593 0.679 ASN A 166 0.837 0.305 0.321 0.784 GLN A 167 0.698 0.743 0.477 0.515 0.870 LEU A 168 0.968 0.640 0.615 0.648 GLU A 169 0.934 0.735 0.564 0.999 0.978 HIS A 170 0.832 0.677 0.359 0.649 HIS A 171 0.810 0.580 0.414 0.845 HIS A 172 0.885 0.450 0.486 0.355 HIS A 173 0.862 0.677 0.482 0.349 HIS A 174 0.873 0.319 0.388 0.515 HIS A 175 0.925 0.736 0.712 Ranges: 8 from: A 4 to A 17 from: A 22 to A 52 from: A 54 to A 73 from: A 76 to A 95 from: A 100 to A 102 from: A 115 to A 116 from: A 119 to A 127 from: A 130 to A 159 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 1 is: 0.911 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 2 is: 0.947 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 3 is: 1.012 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 4 is: 1.194 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 5 is: 0.671 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 6 is: 0.902 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 7 is: 0.852 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 8 is: 0.630 (*) > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 9 is: 0.863 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 10 is: 0.973 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 11 is: 0.748 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 12 is: 0.955 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 13 is: 0.788 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 14 is: 0.713 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 15 is: 0.991 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 16 is: 0.778 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 17 is: 0.769 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 18 is: 0.788 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 19 is: 1.009 > Kabsch RMSD of backbone atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 20 is: 0.965 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..52],[54..73],[76..95],[100..102],[115..116],[119..127],[130..159], is: 0.873 > Range of RMSD values to reference struct. is 0.630 to 1.194 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 1 is: 1.284 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 2 is: 1.234 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 3 is: 1.234 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 4 is: 1.523 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 5 is: 0.958 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 6 is: 1.181 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 7 is: 1.160 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 8 is: 0.885 (*) > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 9 is: 1.088 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 10 is: 1.285 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 11 is: 1.026 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 12 is: 1.205 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 13 is: 1.228 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 14 is: 1.001 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 15 is: 1.265 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 16 is: 1.062 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 17 is: 1.068 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 18 is: 1.149 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 19 is: 1.294 > Kabsch RMSD of heavy atoms in res. A[4..17],A[22..52],A[54..73],A[76..95],A[100..102],A[115..116],A[119..127],A[130..159],for model 20 is: 1.300 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[4..17],[22..52],[54..73],[76..95],[100..102],[115..116],[119..127],[130..159], is: 1.171 > Range of RMSD values to reference struct. is 0.885 to 1.523 PdbStat> PdbStat> *END* of program detected, BYE! ...